webservices/compbio/ws/client/Services.java

   1 /* Copyright (c) 2009 Peter Troshin\r
   2  *  \r
   3  *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0     \r
   4  * \r
   5  *  This library is free software; you can redistribute it and/or modify it under the terms of the\r
   6  *  Apache License version 2 as published by the Apache Software Foundation\r
   7  * \r
   8  *  This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
   9  *  even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
  10  *  License for more details.\r
  11  * \r
  12  *  A copy of the license is in apache_license.txt. It is also available here:\r
  13  * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
  14  * \r
  15  * Any republication or derived work distributed in source code form\r
  16  * must include this copyright and license notice.\r
  17  */\r
  18 \r
  19 package compbio.ws.client;\r
  20 \r
  21 import java.io.File;\r
  22 import java.net.URL;\r
  23 \r
  24 import javax.xml.namespace.QName;\r
  25 import javax.xml.ws.Service;\r
  26 \r
  27 import compbio.data.msa.JABAService;\r
  28 import compbio.data.msa.MsaWS;\r
  29 import compbio.data.msa.SequenceAnnotation;\r
  30 import compbio.engine.client.ConfExecutable;\r
  31 import compbio.engine.client.Executable;\r
  32 import compbio.runner.conservation.AACon;\r
  33 import compbio.runner.disorder.Disembl;\r
  34 import compbio.runner.disorder.GlobPlot;\r
  35 import compbio.runner.disorder.Jronn;\r
  36 import compbio.runner.msa.ClustalW;\r
  37 import compbio.runner.msa.Mafft;\r
  38 import compbio.runner.msa.Muscle;\r
  39 import compbio.runner.msa.Probcons;\r
  40 import compbio.runner.msa.Tcoffee;\r
  41 \r
  42 /**\r
  43  * List of web services currently supported by JABAWS version 2\r
  44  * \r
  45  */\r
  46 public enum Services {\r
  47         MafftWS, MuscleWS, ClustalWS, TcoffeeWS, ProbconsWS, AAConWS, JronnWS, DisemblWS, GlobPlotWS;\r
  48 \r
  49         public static Services getService(String servName) {\r
  50                 servName = servName.trim().toLowerCase();\r
  51                 for (Services service : Services.values()) {\r
  52                         if (service.toString().equalsIgnoreCase(servName)) {\r
  53                                 return service;\r
  54                         }\r
  55                 }\r
  56                 return null;\r
  57         }\r
  58 \r
  59         public static Services getServiceByRunner(\r
  60                         Class<Executable<?>> runnerClassName) {\r
  61                 assert runnerClassName != null;\r
  62                 String sname = runnerClassName.getSimpleName().toLowerCase();\r
  63                 for (Services service : Services.values()) {\r
  64                         if (service.toString().toLowerCase().contains(sname)) {\r
  65                                 return service;\r
  66                         }\r
  67                 }\r
  68                 return null;\r
  69         }\r
  70 \r
  71         public Class<? extends Executable<?>> getServiceImpl() {\r
  72                 switch (this) {\r
  73                         case AAConWS :\r
  74                                 return AACon.class;\r
  75                         case ClustalWS :\r
  76                                 return ClustalW.class;\r
  77                         case MafftWS :\r
  78                                 return Mafft.class;\r
  79                         case MuscleWS :\r
  80                                 return Muscle.class;\r
  81                         case TcoffeeWS :\r
  82                                 return Tcoffee.class;\r
  83                         case ProbconsWS :\r
  84                                 return Probcons.class;\r
  85                         case DisemblWS :\r
  86                                 return Disembl.class;\r
  87                         case GlobPlotWS :\r
  88                                 return GlobPlot.class;\r
  89                         case JronnWS :\r
  90                                 return Jronn.class;\r
  91                         default :\r
  92                                 throw new RuntimeException(\r
  93                                                 "Unknown web service implementation class for service: "\r
  94                                                                 + this);\r
  95                 }\r
  96         }\r
  97 \r
  98         public static Class<? extends Executable<?>> getRunnerByJobDirectory(File jobdir) {\r
  99                 Services service = getServiceByRunnerName(getRunnerNameByJobDirectory(jobdir));\r
 100                 return service.getServiceImpl();\r
 101         }\r
 102 \r
 103         private static String getRunnerNameByJobDirectory(File jobdir) {\r
 104                 String name = jobdir.getName().split("#")[0];\r
 105 \r
 106                 if (name.startsWith(ConfExecutable.CLUSTER_TASK_ID_PREFIX)) {\r
 107                         assert ConfExecutable.CLUSTER_TASK_ID_PREFIX.length() == 1;\r
 108                         name = name.substring(1);\r
 109                 }\r
 110                 return name;\r
 111         }\r
 112 \r
 113         public static Services getServiceByJobDirectory(File jobdir) {\r
 114                 return getServiceByRunnerName(getRunnerNameByJobDirectory(jobdir));\r
 115         }\r
 116 \r
 117         private static Services getServiceByRunnerName(String name) {\r
 118                 for (Services service : Services.values()) {\r
 119                         String runnerName = service.getServiceImpl().getSimpleName()\r
 120                                         .toLowerCase();\r
 121                         name = name.trim().toLowerCase();\r
 122                         if (name.startsWith(runnerName)) {\r
 123                                 return service;\r
 124                         }\r
 125                 }\r
 126                 return null;\r
 127         }\r
 128 \r
 129         Service getService(URL url, String sqname) {\r
 130                 QName qname = new QName(sqname, this.toString());\r
 131                 return Service.create(url, qname);\r
 132         }\r
 133 \r
 134         Class<? extends JABAService> getServiceType() {\r
 135                 switch (this) {\r
 136                         // deliberate leaking\r
 137                         case AAConWS :\r
 138                         case JronnWS :\r
 139                         case DisemblWS :\r
 140                         case GlobPlotWS :\r
 141 \r
 142                                 return SequenceAnnotation.class;\r
 143 \r
 144                                 // deliberate leaking\r
 145                         case ClustalWS :\r
 146                         case MafftWS :\r
 147                         case MuscleWS :\r
 148                         case ProbconsWS :\r
 149                         case TcoffeeWS :\r
 150 \r
 151                                 return MsaWS.class;\r
 152                         default :\r
 153                                 throw new RuntimeException("Unrecognised Web Service Type "\r
 154                                                 + this + " - Should never happened!");\r
 155                 }\r
 156         }\r
 157 \r
 158         JABAService getInterface(Service service) {\r
 159                 assert service != null;\r
 160 \r
 161                 QName portName = new QName(service.getServiceName().getNamespaceURI(),\r
 162                                 this.toString() + "Port");\r
 163                 return service.getPort(portName, this.getServiceType());\r
 164         }\r
 165 }